I think it’s because English isn’t super consistent with the spelling of vowel sounds. Consider also “choose” (rhymes with “lose”) and “chose” (which doesn’t rhyme with either).

I guess really the vowel sound in loose/lose is basically the same; the difference is whether or not the “s” makes a “s” sound or a “z” sound… It is admittely odd that the presence or absence of an extra “o” would affect the sound of an adjacent constant (especially when we have a perfectly good “z” character available).

Which reminds me of my pet peeve: when people use “breath” or “cloth” instead of “breathe” or “clothe”.